Zobrazeno 1 - 10
of 94
pro vyhledávání: '"Douglas L. Brutlag"'
Autor:
Xiaoqiu Huang, Douglas L. Brutlag
Publikováno v:
Nucleic Acids Research
The level of conservation between two homologous sequences often varies among sequence regions; functionally important domains are more conserved than the remaining regions. Thus, multiple parameter sets should be used in alignment of homologous sequ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::01d59e020145cb62b6f286ffe58552e7
http://europepmc.org/articles/PMC1802605
http://europepmc.org/articles/PMC1802605
Autor:
Robert W. Shafer, Soo-Yon Rhee, Douglas L. Brutlag, Jonathan Taylor, Gauhar Wadhera, Asa Ben-Hur
Publikováno v:
Proceedings of the National Academy of Sciences. 103:17355-17360
Understanding the genetic basis of HIV-1 drug resistance is essential to developing new antiretroviral drugs and optimizing the use of existing drugs. This understanding, however, is hampered by the large numbers of mutation patterns associated with
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::83bb44d75428f3361c201bd70c3115aa
https://doi.org/10.1073/pnas.0607274103
https://doi.org/10.1073/pnas.0607274103
Publikováno v:
Nucleic Acids Research
Given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcript
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac4ad4264ff520edcae16a5b6e1bfe73
http://europepmc.org/articles/PMC1635261
http://europepmc.org/articles/PMC1635261
Publikováno v:
ISMB (Supplement of Bioinformatics)
Motivation: DNA motif finding is one of the core problems in computational biology, for which several probabilistic and discrete approaches have been developed. Most existing methods formulate motif finding as an intractable optimization problem and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e54e3f1562e3b01e85d1701178e0acf0
https://doi.org/10.1093/bioinformatics/btl243
https://doi.org/10.1093/bioinformatics/btl243
Autor:
Douglas L. Brutlag, Jessica C. Ebert
Publikováno v:
Bioinformatics. 22:1080-1087
Summary: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments (MSTAs). Consistency-based alignment (CBA) first harnesses the informat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b86b9bcd98e97fcf52ccef755d87f775
https://doi.org/10.1093/bioinformatics/btl046
https://doi.org/10.1093/bioinformatics/btl046
Publikováno v:
Proceedings of the National Academy of Sciences. 103:1412-1417
A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide. CGIs are generally associated with promoters; genes, whose prom
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3390067f6291c2910a90cfcd15d2f08
https://doi.org/10.1073/pnas.0510310103
https://doi.org/10.1073/pnas.0510310103
Publikováno v:
Nucleic Acids Research
Classifying proteins into families and superfamilies allows identification of functionally important conserved domains. The motifs and scoring matrices derived from such conserved regions provide computational tools that recognize similar patterns in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4f7be4ef3271c63444186ff53a2c929
https://doi.org/10.1093/nar/gki060
https://doi.org/10.1093/nar/gki060
Publikováno v:
IEEE Signal Processing Magazine. 21:62-69
The exponential growth of the publicly available data has transformed biology into an information rich science that provides new and interesting applications for the machine learning community. In this article, the author presents some specific examp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::cf17bd89d94849701a7e95842f954f26
https://doi.org/10.1109/msp.2004.1359143
https://doi.org/10.1109/msp.2004.1359143
Publikováno v:
Nucleic Acids Research. 32:W204-W207
The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs-sampling-based program for predicti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e09e8dd8d750826aa00817d57c04dd7
https://doi.org/10.1093/nar/gkh461
https://doi.org/10.1093/nar/gkh461
Autor:
Jessica Shapiro, Douglas L. Brutlag
Publikováno v:
Protein Science. 13:278-294
We report an unsupervised structural motif discovery algorithm, FoldMiner, which is able to detect global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classific
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2449cab3499e709acb0959f615e370e3
https://doi.org/10.1110/ps.03239404
https://doi.org/10.1110/ps.03239404